Phantom Who
by PhantomWorks- Stories division
Summary: Doctor who and marvel crossover. During the last days in the time war several genticly engineered babies were sent by the genetic prototype and his father to earth to keep them safe- but they didnt know about CBI. I own nothing.


**And the man with only a basic plan has returned. When I was talking last time I said that this story would be a post last of us story. I have since changed my mind. Now the storey take's place within the last of us. Regardless everything in the cover but Ellie belongs to Danny. We have;**

**- A set of goggles and an earpiece that can transform into star lord's helmet from guardians of the galaxy.**

**- A wrist mounted computer display/ communications device.**

**- A larger computerised device that rolls up into a built in storage space.**

**- A TARDIS key.**

**- A sonic screwdriver**

**- A holographic emitter disguised as a galifrayan pocket watch.**

**- A customised type 40 TARDIS (Not the doctor's TARDIS but a new one).**

**- Though not pictured he has a psychic paper wallet like his late father, The Doctor.**

**Anyway onto chapter 1.**

_**Chapter 1 first contact**_

Joel Miller was a smuggler. He and his partner Tess had been hunting down a trader named Robert who had stolen weapons from them and, upon confrontation with them was killed after revealing that he had sold these weapons to the militia group the fireflies. Immediately afterwards the leader of the Fireflies Marlene had approached them and told them that they could have their guns and more if they smuggled something out of Boston.

They agreed and this led to them meeting Ellie miller and Danny Fenton. 2 children of just 14 years old. Ellie was a girl with a relatively innocent look on the world. She also however was not unwilling to get violent or swear. Danny was different, while still a fighter he seemed to be more knowledgeable about the dark side of life but hid it beneath a light-hearted mask.

While Marlene and Tess went to confirm the weapons Joel took the 2 children back to his apartment. While Ellie remained tight lipped on why she was there it was clear why Danny had caught Marlene's attention; the kid was a genius. Also he possessed technology more advanced than 2013 but refused to tell people where he got it.

Joel was currently resting while Danny and Ellie attempted to entertain themselves. When he awoke he saw Ellie reading while Danny was playing with a bouncy ball. Tess opened the door.

"I've seen the goods. It's a lot. Are we goanna do this?" she asked. Joel nodded, sighing. He had avoided children, particularly girls around 12, after his daughter was killed by a soldier 20 year ago the day of the outbreak.

* * *

><p>Coming out of the tunnel Ellie's eyes sparkled. "Whoa. I've never been outside before." She muttered, to Joel's chagrin.<p>

"It was better before the outbreak." Danny said, absent minded.

"How would you know?" Tess asked sharply.

"Um, I saw some pictures?" He said nervously. **(Actually he has the doctor's memories of earth.)**

"Whatever. Up here." Joel said as he climbed up through an old shipping container.

"Hold it!" the 4 froze as they found themselves cornered by 2 soldiers.

"Crud." Danny whispered as they were lined up and scanned. Tess Joel and Danny scanned clean but as Ellie was scanned she attacked the 2 men and the2 smugglers shot them.

"Holy s***!" Ellie exclaimed looking at the 2 soldiers. Before she could continue Tess grabbed her and backed her up onto a shipping container.

"Marlene set us up." She told Joel handing him the scanner.

"Want to explain why we're carrying an infected child?" Danny's eyes widened.

"What! That's impossible! I've known Ellie for a week and she wasn't bitten within that time. And from what I understand of the infection and everything she would have turned ages ago."

"It's true. I'm immune. I was bitten 3 weeks ago. Look!" she pulled up her sleeve to show a bite mark on her arm. It look like it was a few minutes old from the fungal appearance but the bite itself had scabbed over, sowing it to be much older. "Marlene thinks they can study this to create an antidote."

"Wait." Tess said as they realised what Danny had said. "You said 'What I understand of the infection'. Everyone knows about the infection, you learn enough of it at age 10, why did you not?"

Danny looked around before sighing. "I didn't know because I wasn't on earth 4 years ago." He said.

"What?" Joel said.

"I'm a time lord 2.0 from the planet galifray. As the name suggests I am a time traveller. And I'm not sure Ellie but I think you might be one to."

"What? Why?" Ellie asked.

"Cause when we met I felt something familiar inside. A familiar presence. And it would explain your immunity because before I knew about the infection I inhaled a ton of spores. The fungus doesn't affect time lords."

"But why would I be here. My mother found me as a baby. Why would I be in Boston and not back home?" Ellie asked.

"Cause me and my dad sent you and the others somewhere safe. At least we thought it was safe." Danny said.

"Why?"

"Because we were in the middle of the last days of a war, we didn't want a group of newborns in danger. My dad had already lost al his friends and his ship we didn't want to put you guys at risk."

"Others?" Joel asked.

"Yeah, the lab had a load of genetically engineered babies." Danny said.

"Why did you genetically engineer babies?" Tess asked.

"I didn't, I was a prisoner and the only pre-existing test subject to survive the tests." Danny said.

"Well still why?" Joel asked.

"Why did Erskine make captain America?" Danny asked in response. "Let's move."

* * *

><p>The group had managed to sneak past the army and were in a subterranean tunnel.<p>

"Hey Danny." Ellie asked

"Yup." The young time lord replied.

"How'd you end up here?"

"Well it's a long story. Firstly years ago my dad grew tired of the non-intervention policy of our people and ran away. In time he was caught and forced on several missions. One involved neutralising a cyborg species called the Dalek literally bred for war at the moment of their creation. Due to the unity this race had brought against themselves he was unable to do it. However years later they learnt of this plot and attacked the time lords. Eventually he himself regenerated into a war like version of himself but, before he could pull the ultimate trigger his body failed him and he regenerated into a normal him. Filled with grief over his actions he couldn't do it but he learnt of the lab and, with his ship's last journey, he found it and freed me as a monster killed the staff. We sent you to earth to be adopted, unaware of any of this, and started building a new ship for me that we were goanna use to put our planet in a stasis dimension to save it. However before he could finish the mission he was shot and killed. I was the one who finished it but the chronotemporal turbulence sent me into the skies miles above America about a month ago. I fell out of my ship and dropped my screwdriver and wound up in a spore filled room. I was unconscious for several days. That's how I knew I was immune. Eventually. Any questions?" Danny asked.

"I have a few." Ellie said.

"Go ahead."

"What is a cyborg?"

"An organic being modified with technology."

"What' regenerate?"

"Time lord 1.0s could renew their body 12 times when they die but it changes their appearance and personality. 2.0s have no limit and don't change."

"What's with the screwdriver?"

"My sonic screwdriver, a time lord omnitool. Joel do you remember how hitchhikers guide to the galaxy tells you to always know where your towel is? (He nodded) It's like that for us with sonic screwdrivers."

"What's your ship called?"

"T-A-R-D-I-S Time And Relative Dimensions In Space known as TARDIS."

"You said that you and, potentially, I are upgraded species, how exactly?"

"We can transform into a ghost form with uncountable Powers, we have technopathy and when unlocked we have an incredible intellect."

"How will we know?"

"When I Find my screwdriver I can scan you and find out."

"Hold up." Joel interrupted the QnA session. "Damn it clicker." He said examining the corpse with a massively mutated head.

"What's wrong with it's head?" Ellie asked.

"It's what happens if you are infected for long enough." Joel explained.

"I'm guessing it uses echolocation, like a bat." Danny summarised, having examined the head.

"Yup." Tess said. "Stay quiet and stay low." Danny and Ellie nodded.

* * *

><p>The group were nearly at the capitol building.<p>

"Hey if you have all this power why haven't you used any of it?" Ellie asked.

Danny shrugged.

"I was wounded in re-entry my core, which provides my Powers, was locked, until I use my screwdriver to unlock it I have technopathy, strength, intelligence and healing and, though my cloves a made of technopathicly controlled nanotech they are glitched out and I need the screwdriver to fix it. Basically I'm at low power till I figure out where that screwdriver is. I know it landed somewhere outside of Boston in this direction but I don't know where exactly."

"Hey did the lab make anything else?"

"They made a race called night furies, kind of like dragons, though none had hatched when I put the eggs in the hatchery back in the TARDIS and I built a sentient robot named Metabee but he is inactive right now." Danny said.

Then they turned into the courtyard to see it was flooded.

"Um, I can't swim." Ellie said nervously.

"Seriously?" Danny asked.

"I'm an orphan thrown into a military school, no one bothered to teach me."

"The TARDIS has a pool, I'll teach you."

"Thanks."

"If you to lovebirds are quite done I isn't too deep." Joel said. "We can wade through."

The 2 teens immediately started walking blushing furiously.

When they got in to the building they saw the fireflies dead on the floor.

"No. No, no, no." Tess muttered as she walked up to them. She was desperately searching for something to tell them what to do next.

"I don't know where the lab is and if Danny's right it wouldn't do any good." Ellie said.

"Then what do we do?" Tess yelled.

"Find the screwdriver. We are close; my watch is picking it up now. With it we can get me and my gear working again and find the TARDIS." Danny said.

"And what? Go back and stop the f***ing outbreak?" Joel yelled.

"Sadly no, this is apparently fixed time, I can't undo it. But I can find a way to destroy this stuff." Danny replied calmly.

"Really? What the hell are we doing here Tess? Why are we risking our lives like this?"

"BECAUSE MINE'S ALREADY OVER!" Tess yelled.

"You're infected aren't you." Danny said flatly. Tess nodded.

"Please Joel, do this for me." She pleaded.

"Even if I do it won't save you, it won't bring you back. It-it won't bring back my daughter!" he yelled, one job and his life is falling down the drain.

"Your daughter?" Danny asked.

"The day of the outbreak a soldier shot her. She disappeared into a bright light before she died."

"This light, was it sort of a vortex of colour?"

"Yes."

"Then you're wrong on both counts. If I can get to the TARDIS then I can bring both of them back."

"What? Danny Sarah's been dead for years and I will be either dead or turned."

"And the TARDIS has excellent medical technology and a machine that can literally pull people from any point in time. I can pull you there and save you. Same with Sarah" he looked at Joel.

"You can really do that you can bring her back to me?" For the first time in 20 years Joel miller felt hope.

"From what you described I already did." Danny said.

Soldiers were knocking at the door behind the group. Tess stepped forward.

"You guys go. I'll hold them off." Tess told her friend.

"See you in the future." Danny said as they ran off.

* * *

><p><strong>And here we are, Tess is bitten but Danny has found a way to save her and Sarah! If you were curious the TARDIS is in Wyoming near Tommy's dam. Next chapter will feature more. And yes this is DannyEllie I've only written the beginning of one story for this pairing, of which I am the only current shipper, and I'm already hooked. Then I believe I am the spear header for several pairings (Danny/Cat from victorious, Danny/Penny from Bolt and Dani/Bumblebee from transformers) anyway I will probably work on Halfa Cure by the time you guys get this along with possible additions to The Phantom Knight and the first of them.**

**Next chapter will start Bill's part. It will also feature the sonic screwdriver; introduced in what I reckon will be a funny way.**


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